Sequence
atgc intronic sequence ATGC exonic sequence...gttgccaagaatccgctcatgcttgattgttgacggtgttatgtccatattggatttagaatgtgcagagactacagttttggttgattacaatttgcagGAATTCAATGGCTTCATAGCAGGATAGATATCAATGGTTATGAGGAGTATAGTGGTACTGAGTACCGGTCAGCTGGATGTACTGAGGAATACAATGTCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23640.2 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: LOC_Os07g23880.1 (Oryza sativa), 3'ss of exon 18
-gttgccaagaatcc---gctcatgcttgattg--ttgacggtgttatgtccatattggatttagaatgtgcagagactacagttttggttgattacaatttgcagGAATTCAATGGCTTCATAGCAGGATAGATATCAATGGTTATGAGGAGTATAGTGGTACTGAGTACCGGTCAGCTGGATGTACTGAGGAATACAATGTCAT
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aattctgaaagaaccaaaagttatgacttactagctcaagtatattaattaaaaattgctttcaaaaggtg-acagtttctctttttgttggatta-----tgcagATTCCCAGTGGCTTCATAGCAGGATTGAAATCAATGGTTATGAAGAATACAGTGGGACTGAATATAGGTCCGCTGGATGCACTGAAGAATACAATGTCAT
upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA04G14810.1 (Glycine max), 3'ss of exon 18
-----------------------------------gttgccaagaatccgctcat-gcttg-attgttgacggtgttatgtccat-attggatttagaatgtgcagaga-----ctacagttttggt--tgatta-caatttg---cagGAATTCAATGGCTTCATAGCAGGATAGATATCAATGGTTATGAGGAGTATAGTGGTACTGAGTACCGGTCAGCTGGATGTACTGAGGAATACAATGTCAT
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gtacgttgatcataattcgcaatatatttaatttgtttattggaaatgtacaagtagcttgtgtttttccctgtgacacattgattaaataatttgtattgtttataatatgctttacaatgttcatgataataaacaatttttttcagGAACACAATGGCTCCATAGTAGGATTGAGATAAATGGGTATGAGGAGTATAGTGGTATGGAGTATCGTTCTGCTGGGTGTTCTGAGGAATATTCTGTCAT
upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv02s0033g01410.t01 (Vitis vinifera), 3'ss of exon 19
gttgccaagaatccgctcatgcttgattgttgacggt-gttatgtccat-attggatttagaatgtgcagagactacagttttggttgattacaatttgcagGAATTCAATGGCTTCATAGCAGGATAGATATCAATGGTTATGAGGAGTATAGTGGTACTGAGTACCGGTCAGCTGGATGTACTGAGGAATACAATGTCAT
|| ||| | ||| | | | | || ||| | | | || ||| | | | || || | | | | ||| | ||| |||||| ||| ||||||||||||||||| || ||||| ||||| || || |||||| ||||||||||||||||||||| |||||||||| | | |
-ttctcaaaactccttaagtcaactaatttagatggttggaacatgaattatttgccatgaattgaccatgtcttcctctcctatatgagcaatgttt-cagGAACTCAGTGGCTTCATAGCAGGATTGAAGCTAATGGATATGAAGAATACAGTGGTGTTGAGTACCGGTCAGCTGGATGGTCTGAGGAATATACCATTGT
upper sequence: AT3G23640.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv02s0087g00030.t01 (Vitis vinifera), 3'ss of exon 8
gttgccaagaatccgctcatgcttgattgttgacggt-gttatgtccat-attggatttagaatgtgcagagactacagttttggttgattacaatttgcagGAATTCAATGGCTTCATAGCAGGATAGATATCAATGGTTATGAGGAGTATAGTGGTACTGAGTACCGGTCAGCTGGATGTACTGAGGAATACAATGTCAT
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-ttctcaaagctccttaaatcaactaatttagatggttggaacatgaattatttgccatgagttgaccatgtcttcctctcctatatgaacattgttt-cagGAACTCAATGGCTTCATAGCAAGATTGAAGCTAATGGATATGGAGAATATAGTGGTGTTGAGTACTGGTCAGCTGGATGGTCTGAGGAATATACCATTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catattggatttagaatgtgcagagactacagttttggttgattacaatttgcagGAATTCAATGGCTTCATAGCAGGATAGATATCAATGGTTATGAGGAGTATAGTGGTACTGAGTACCGGTCAGCTGGATGTACTGAGGAATACAATGTCAT
ggttgat putative branch site (score: 5)
attacaattt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgccaagaatccgctcatgcttgattgttgacggtgttatgtccatattggatttagaatgtgcagagactacagttttggttgattacaatttgcagGAATTCAATGGCTTCATAGCAGGATAGATATCAATGGTTATGAGGAGTATAGTGGTACTGAGTACCGGTCAGCTGGATGTACTGAGGAATACAATGTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA